Omenn Gilbert S
Departments of Medicine and Genetics, Center for Computational Medicine and Bioinformatics, Medical School and School of Public Health, University of Michigan, Ann Arbor, MI, USA.
Methods Mol Biol. 2011;696:247-57. doi: 10.1007/978-1-60761-987-1_15.
The Human Plasma Proteome Project (HPPP) is an international collaboration coordinated by the Human Proteome Organisation (HUPO). Its Pilot Phase generated the 2005 Proteomics special issue "Exploring the Human Plasma Proteome" (Omenn et al. Proteomics 5:3226-3245, 2005) and a book with the same title (Omenn GS (ed) (2006) Exploring the human plasma proteome. Wiley-Liss, Weinheim, pp 372). Data management for that Pilot Phase included collection, integration, analysis, and dissemination of findings from participating laboratories and data repositories. Many investigators face the same challenges of integration of data from complex, dynamic serum, and plasma specimens. The PPP workflow assembled a representative Core Dataset of 3,020 protein identifications, overcoming ambiguity and redundancy in the heterogeneous contributed identifications and redundancy and updates in the protein sequence databases. The results were made available with alternative thresholds from the University of Michigan, yielding a range of numbers of protein identifications. Data were submitted to EBI/PRIDE and to ISB/PeptideAtlas. The current phase of the PPP employs Proteome Xchange to link submission of well-annotated primary datasets to EBI/PRIDE, distributed file sharing by Tranche/Proteome Commons.org, and reanalysis from the primary raw spectra at ISB/PeptideAtlas. Such human plasma proteome datasets are available for data mining comparisons with the proteomes of other organs and biofluids in health and disease.
人类血浆蛋白质组计划（HPPP）是一项由人类蛋白质组组织（HUPO）协调的国际合作项目。其试点阶段产生了2005年蛋白质组学特刊《探索人类血浆蛋白质组》（奥门等人，《蛋白质组学》5:3226 - 3245，2005年）以及一本同名书籍（奥门GS（编）（2006年）《探索人类血浆蛋白质组》。威利 - 利斯出版社，魏因海姆，第372页）。该试点阶段的数据管理包括收集、整合、分析以及传播参与实验室和数据存储库的研究结果。许多研究人员面临着整合来自复杂、动态血清和血浆样本数据的相同挑战。PPP工作流程汇集了一个包含3020个蛋白质鉴定结果的代表性核心数据集，克服了异质贡献鉴定中的模糊性和冗余性以及蛋白质序列数据库中的冗余性和更新问题。研究结果在密歇根大学以不同阈值提供，产生了一系列蛋白质鉴定数量。数据已提交至EBI/PRIDE和ISB/PeptideAtlas。PPP的当前阶段采用蛋白质组交换联盟将注释良好的原始数据集提交与EBI/PRIDE相链接，通过Tranche/Proteome Commons.org进行分布式文件共享，并在ISB/PeptideAtlas对原始质谱进行重新分析。此类人类血浆蛋白质组数据集可用于与健康和疾病状态下其他器官及生物流体的蛋白质组进行数据挖掘比较。
